NAME

       Bio::Search::Result::CrossMatchResult - CrossMatch-specific subclass of
       Bio::Search::Result::GenericResult

SYNOPSIS

           # Working with iterations (CrossMatch results)

           $result->next_iteration();
           $result->num_iterations();
           $result->iteration();
           $result->iterations();

       # See Bio::Search::Result::GenericResult for information about working with Results.

       # See Bio::Search::Iteration::IterationI # for details about working with iterations.

       # TODO: #     * Show how to configure a SearchIO stream so that it generates #
       CrossMatchResult objects.

DESCRIPTION

       This object is a subclass of Bio::Search::Result::GenericResult and provides some
       operations that facilitate working with CrossMatch and CrossMatch results.

       For general information about working with Results, see
       Bio::Search::Result::GenericResult.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to the Bioperl mailing list.  Your participation
       is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their
       resolution. Bug reports can be submitted via the web:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR - Shin Leong

       Email sleong@watson.wustl.edu

CONTRIBUTORS

       Additional contributors names and emails here

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

   new
        Title   : new
        Usage   : my $obj = Bio::Search::Result::CrossMatchResult->new();
        Function: Builds a new Bio::Search::Result::CrossMatchResult object
        Returns : Bio::Search::Result::CrossMatchResult
        Args    : See Bio::Search::Result::GenericResult();
                  The following parameters are specific to CrossMatchResult:
                    -iterations  => array ref of Bio::Search::Iteration::IterationI objects
                    -inclusion_threshold => e-value threshold for inclusion in the
                                            CrossMatch score matrix model (blastpgp)

   hits
       This method overrides Bio::Search::Result::GenericResult::hits to take into account the
       possibility of multiple iterations, as occurs in CrossMatch reports.

       If there are multiple iterations, all 'new' hits for all iterations are returned.  These
       are the hits that did not occur in a previous iteration.

       See Also: Bio::Search::Result::GenericResult::hits

   next_hit
       This method overrides Bio::Search::Result::GenericResult::next_hit to take into account
       the possibility of multiple iterations, as occurs in CrossMatch reports.

       If there are multiple iterations, calling next_hit() traverses the all of the hits, old
       and new, for each iteration, calling next_hit() on each iteration.

       See Also: Bio::Search::Iteration::GenericIteration::next_hit

   num_hits
       This method overrides Bio::Search::Result::GenericResult::num_hits to take into account
       the possibility of multiple iterations, as occurs in CrossMatch reports.

       If there are multiple iterations, calling num_hits() returns the number of 'new' hits for
       each iteration. These are the hits that did not occur in a previous iteration.

       See Also: Bio::Search::Result::GenericResult::num_hits

   add_iteration
        Title   : add_iteration
        Usage   : $report->add_iteration($iteration)
        Function: Adds a IterationI to the stored list of iterations
        Returns : Number of IterationI currently stored
        Args    : Bio::Search::Iteration::IterationI

   next_iteration
        Title   : next_iteration
        Usage   : while( $it = $result->next_iteration()) { ... }
        Function: Returns the next Iteration object, representing all hits
                  found within a given CrossMatch iteration.
        Returns : a Bio::Search::Iteration::IterationI object or undef if there are no more.
        Args    : none

   iteration
        Usage     : $iteration = $blast->iteration( $number );
        Purpose   : Get an IterationI object for the specified iteration
                    in the search result (CrossMatch).
        Returns   : Bio::Search::Iteration::IterationI object
        Throws    : Bio::Root::NoSuchThing exception if $number is not within
                    range of the number of iterations in this report.
        Argument  : integer (optional, if not specified get the last iteration)
                    First iteration = 1

   num_iterations
        Usage     : $num_iterations = $blast->num_iterations;
        Purpose   : Get the number of iterations in the search result (CrossMatch).
        Returns   : Total number of iterations in the report
        Argument  : none (read-only)

   number_of_iterations
       Same as num_iterations.

   round
       Same as iteration.

   iterations
        Title   : iterations
        Usage   : my @iterations = $result->iterations
        Function: Returns the IterationI objects contained within this Result
        Returns : Array of L<Bio::Search::Iteration::IterationI> objects
        Args    : none

   no_hits_found
        Usage     : $nohits = $blast->no_hits_found( $iteration_number );
        Purpose   : Get boolean indicator indicating whether or not any hits
                    were present in the report.

                    This is NOT the same as determining the number of hits via
                    the hits() method, which will return zero hits if there were no
                    hits in the report or if all hits were filtered out during the parse.

                    Thus, this method can be used to distinguish these possibilities
                    for hitless reports generated when filtering.

        Returns   : Boolean
        Argument  : (optional) integer indicating the iteration number (CrossMatch)
                    If iteration number is not specified and this is a CrossMatch result,
                    then this method will return true only if all iterations had
                    no hits found.

   set_no_hits_found
        Usage     : $blast->set_no_hits_found( $iteration_number );
        Purpose   : Set boolean indicator indicating whether or not any hits
                    were present in the report.
        Returns   : n/a
        Argument  : (optional) integer indicating the iteration number (CrossMatch)

   _next_iteration_index
        Title   : _next_iteration_index
        Usage   : private

   rewind
        Title   : rewind
        Usage   : $result->rewind;
        Function: Allow one to reset the Iteration iterator to the beginning
                  Since this is an in-memory implementation
        Returns : none
        Args    : none

   inclusion_threshold
        Title   : inclusion_threshold
        Usage   : my $incl_thresh = $result->inclusion_threshold; (read-only)
        Function: Gets the e-value threshold for inclusion in the CrossMatch
                  score matrix model (blastpgp) that was used for generating the report
                  being parsed.
        Returns : number (real) or undef if not a CrossMatch report.
        Args    : none